Read the Docs build information Build id: 48999 Project: cyverse-atmosphere-guide Version: latest Commit: 086d632275de2bd7d7f7fae64855f9108c240667 Date: 2017-06-09T22:17:18.877512Z State: finished Success: True [rtd-command-info] start-time: 2017-06-10T03:16:59.322636Z, end-time: 2017-06-10T03:17:00.984744Z, duration: 1, exit-code: 0 python2.7 -mvirtualenv --no-site-packages --no-download New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/envs/latest/bin/python2.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/envs/latest/bin/python Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2017-06-10T03:17:01.093569Z, end-time: 2017-06-10T03:17:30.313973Z, duration: 29, exit-code: 0 python pip install --use-wheel -U --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip sphinx==1.5.3 Pygments==2.2.0 setuptools==28.8.0 docutils==0.13.1 mkdocs==0.15.0 mock==1.0.1 pillow==2.6.1 readthedocs-sphinx-ext<0.6 sphinx-rtd-theme<0.3 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 Collecting sphinx==1.5.3 Downloading Sphinx-1.5.3-py2.py3-none-any.whl (1.6MB) Collecting Pygments==2.2.0 Downloading Pygments-2.2.0-py2.py3-none-any.whl (841kB) Requirement already up-to-date: setuptools==28.8.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/envs/latest/lib/python2.7/site-packages Collecting docutils==0.13.1 Downloading docutils-0.13.1-py2-none-any.whl (537kB) Collecting mkdocs==0.15.0 Downloading mkdocs-0.15.0-py2.py3-none-any.whl (966kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861kB) Collecting pillow==2.6.1 Downloading Pillow-2.6.1.zip (7.5MB) Collecting readthedocs-sphinx-ext<0.6 Downloading readthedocs_sphinx_ext-0.5.5-py2.py3-none-any.whl Collecting sphinx-rtd-theme<0.3 Downloading sphinx_rtd_theme-0.2.4-py2.py3-none-any.whl (1.4MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.10-py2.py3-none-any.whl Collecting commonmark==0.5.4 Downloading CommonMark-0.5.4.tar.gz (120kB) Collecting recommonmark==0.4.0 Downloading recommonmark-0.4.0-py2.py3-none-any.whl Collecting six>=1.5 (from sphinx==1.5.3) Downloading six-1.10.0-py2.py3-none-any.whl Collecting requests>=2.0.0 (from sphinx==1.5.3) Downloading requests-2.17.3-py2.py3-none-any.whl (87kB) Collecting imagesize (from sphinx==1.5.3) Downloading imagesize-0.7.1-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx==1.5.3) Downloading Babel-2.4.0-py2.py3-none-any.whl (6.8MB) Collecting snowballstemmer>=1.1 (from sphinx==1.5.3) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB) Collecting Jinja2>=2.3 (from sphinx==1.5.3) Downloading Jinja2-2.9.6-py2.py3-none-any.whl (340kB) Collecting tornado>=4.1 (from mkdocs==0.15.0) Downloading tornado-4.5.1.tar.gz (483kB) Collecting click>=4.0 (from mkdocs==0.15.0) Downloading click-6.7-py2.py3-none-any.whl (71kB) Collecting livereload>=2.3.2 (from mkdocs==0.15.0) Downloading livereload-2.5.1-py2-none-any.whl Collecting mkdocs-bootstrap>=0.1.1 (from mkdocs==0.15.0) Downloading mkdocs-bootstrap-0.1.1.tar.gz (363kB) Collecting mkdocs-bootswatch>=0.1.0 (from mkdocs==0.15.0) Downloading mkdocs-bootswatch-0.4.0.tar.gz (4.4MB) Collecting PyYAML>=3.10 (from mkdocs==0.15.0) Downloading PyYAML-3.12.tar.gz (253kB) Collecting Markdown>=2.3.1 (from mkdocs==0.15.0) Downloading Markdown-2.6.8.tar.gz (307kB) Collecting nilsimsa>=0.3.7 (from readthedocs-sphinx-ext<0.6) Downloading nilsimsa-0.3.8.tar.gz (276kB) Collecting idna<2.6,>=2.5 (from requests>=2.0.0->sphinx==1.5.3) Downloading idna-2.5-py2.py3-none-any.whl (55kB) Collecting urllib3<1.22,>=1.21.1 (from requests>=2.0.0->sphinx==1.5.3) Downloading urllib3-1.21.1-py2.py3-none-any.whl (131kB) Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx==1.5.3) Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB) Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx==1.5.3) Downloading certifi-2017.4.17-py2.py3-none-any.whl (375kB) Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.5.3) Downloading pytz-2017.2-py2.py3-none-any.whl (484kB) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.5.3) Downloading MarkupSafe-1.0.tar.gz Collecting singledispatch (from tornado>=4.1->mkdocs==0.15.0) Downloading singledispatch-3.4.0.3-py2.py3-none-any.whl Collecting backports_abc>=0.4 (from tornado>=4.1->mkdocs==0.15.0) Downloading backports_abc-0.5-py2.py3-none-any.whl Building wheels for collected packages: mock, pillow, commonmark, tornado, mkdocs-bootstrap, mkdocs-bootswatch, PyYAML, Markdown, nilsimsa, MarkupSafe Running setup.py bdist_wheel for mock: started Running setup.py bdist_wheel for mock: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/b2/f8/fe/920b7d3b279878045354cde14646f73864cf944501f19e4a1b Running setup.py bdist_wheel for pillow: started Running setup.py bdist_wheel for pillow: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/d0/3d/6f/4a3dbe290c7053073e6c32734c146d7174f2ad7675030b6137 Running setup.py bdist_wheel for commonmark: started Running setup.py bdist_wheel for commonmark: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/fd/3a/ea/9ead7944d8ba3771888487ca4f6ef39bcde9fd4e986c32f442 Running setup.py bdist_wheel for tornado: started Running setup.py bdist_wheel for tornado: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/84/83/cd/6a04602633457269d161344755e6766d24307189b7a67ff4b7 Running setup.py bdist_wheel for mkdocs-bootstrap: started Running setup.py bdist_wheel for mkdocs-bootstrap: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/6a/6b/d4/b947c6453aae64d38ab0e3b70cb71a60cb6bb7d0a184a4b727 Running setup.py bdist_wheel for mkdocs-bootswatch: started Running setup.py bdist_wheel for mkdocs-bootswatch: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/cd/af/36/fbd242260aeadfc4d890450b2070d4e42ea129460d771d0e37 Running setup.py bdist_wheel for PyYAML: started Running setup.py bdist_wheel for PyYAML: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/2c/f7/79/13f3a12cd723892437c0cfbde1230ab4d82947ff7b3839a4fc Running setup.py bdist_wheel for Markdown: started Running setup.py bdist_wheel for Markdown: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/85/a7/08/33ee5cd488d0365d8bed79d1d4e5c28dd3fbfc7f6d0ad4bb09 Running setup.py bdist_wheel for nilsimsa: started Running setup.py bdist_wheel for nilsimsa: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/77/f8/25/539c7b52ecbfcb7ed9b6c7189f9fdde48706c41fe529a64c9f Running setup.py bdist_wheel for MarkupSafe: started Running setup.py bdist_wheel for MarkupSafe: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57 Successfully built mock pillow commonmark tornado mkdocs-bootstrap mkdocs-bootswatch PyYAML Markdown nilsimsa MarkupSafe Installing collected packages: six, idna, urllib3, chardet, certifi, requests, docutils, Pygments, imagesize, pytz, babel, snowballstemmer, MarkupSafe, Jinja2, alabaster, sphinx, singledispatch, backports-abc, tornado, click, livereload, mkdocs-bootstrap, mkdocs-bootswatch, PyYAML, Markdown, mkdocs, mock, pillow, nilsimsa, readthedocs-sphinx-ext, sphinx-rtd-theme, commonmark, recommonmark Successfully installed Jinja2-2.9.6 Markdown-2.6.8 MarkupSafe-1.0 PyYAML-3.12 Pygments-2.2.0 alabaster-0.7.10 babel-2.4.0 backports-abc-0.5 certifi-2017.4.17 chardet-3.0.4 click-6.7 commonmark-0.5.4 docutils-0.13.1 idna-2.5 imagesize-0.7.1 livereload-2.5.1 mkdocs-0.15.0 mkdocs-bootstrap-0.1.1 mkdocs-bootswatch-0.4.0 mock-1.0.1 nilsimsa-0.3.8 pillow-2.6.1 pytz-2017.2 readthedocs-sphinx-ext-0.5.5 recommonmark-0.4.0 requests-2.17.3 singledispatch-3.4.0.3 six-1.10.0 snowballstemmer-1.2.1 sphinx-1.5.3 sphinx-rtd-theme-0.2.4 tornado-4.5.1 urllib3-1.21.1 [rtd-command-info] start-time: 2017-06-10T03:17:32.416064Z, end-time: 2017-06-10T03:17:32.516127Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'YOUR PROJECT NAME HERE as topic_tutorial' copyright = '2016, CyVerse' author = 'your_name' version = '1.0' release = '1.0' epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix else: SUFFIX = source_suffix[0] else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = 'https://media.readthedocs.com/' else: websupport2_static_url = 'https://media.readthedocs.com/media//static' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/cyverse-atmosphere-guide/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'cyverse-atmosphere-guide', 'name': u'atmosphere_guide', 'rtd_language': u'en', 'canonical_url': 'https://cyverse-atmosphere-guide.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/./', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'atmosphere_guide', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '086d6322', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): extensions.append("readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2017-06-10T03:17:32.687396Z, end-time: 2017-06-10T03:17:33.847550Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.5.3 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] index reading sources... [ 66%] step1 reading sources... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step3' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step4' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step5' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:68: ERROR: Unknown target name: "icommands quick start <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:69: ERROR: Unknown target name: "icommands download links <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done writing output... [ 33%] index writing output... [ 66%] step1 writing output... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index generating indices... genindex writing additional pages... search copying images... [ 33%] ./img/atmosphere/atmosphere-icon.png copying images... [ 66%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 18 warnings. [rtd-command-info] start-time: 2017-06-10T03:17:33.991341Z, end-time: 2017-06-10T03:17:34.965802Z, duration: 0, exit-code: 0 python sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json Running Sphinx v1.5.3 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [json]: targets for 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] index reading sources... [ 66%] step1 reading sources... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step3' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step4' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step5' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:68: ERROR: Unknown target name: "icommands quick start <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:69: ERROR: Unknown target name: "icommands download links <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done writing output... [ 33%] index writing output... [ 66%] step1 writing output... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index generating indices... genindex writing additional pages... search copying images... [ 33%] ./img/atmosphere/atmosphere-icon.png copying images... [ 66%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 15 warnings. [rtd-command-info] start-time: 2017-06-10T03:17:35.179703Z, end-time: 2017-06-10T03:17:36.211066Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.5.3 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] index reading sources... [ 66%] step1 reading sources... [100%] step2 looking for now-outdated files... none found pickling environment... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step3' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step4' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step5' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:68: ERROR: Unknown target name: "icommands quick start <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:69: ERROR: Unknown target name: "icommands download links <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done assembling single document... step1 step2 writing... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index done writing additional files... copying images... [ 33%] ./img/atmosphere/atmosphere-icon.png copying images... [ 66%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded, 15 warnings. [rtd-command-info] start-time: 2017-06-10T03:17:36.420301Z, end-time: 2017-06-10T03:17:37.304348Z, duration: 0, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.5.3 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] index reading sources... [ 66%] step1 reading sources... [100%] step2 looking for now-outdated files... none found pickling environment... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step3' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step4' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step5' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:68: ERROR: Unknown target name: "icommands quick start <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:69: ERROR: Unknown target name: "icommands download links <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png done checking consistency... done processing CyVerseDocumentation.tex... index step1 step2 resolving references... writing... done copying images... ./img/atmosphere/atmosphere-icon.png ./img/homeicon.png ./img/cyverse_rgb.png copying TeX support files... done build succeeded, 11 warnings. [rtd-command-info] start-time: 2017-06-10T03:17:37.538452Z, end-time: 2017-06-10T03:17:38.114006Z, duration: 0, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/chec kouts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2016/10/12 v1.5 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/threeparttable/threeparttable.sty) (./footnotehyper-sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/mdwtools/footnote.sty)) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/pdftex/pdfcolor.tex) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (./needspace.sty) ** (sphinx) defining (legacy) text style macros without \sphinx prefix ** if clashes with packages, set latex_keep_old_macro_names=False in conf.py (./sphinxhighlight.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty) (/usr/share/texlive/texmf-dist/tex/latex/eqparbox/eqparbox.sty (/usr/share/texlive/texmf-dist/tex/latex/environ/environ.sty (/usr/share/texlive/texmf-dist/tex/latex/trimspaces/trimspaces.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx No file CyVerseDocumentation.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1 <./cyverse_r gb.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3 <./atmosphere-ico n.png>] LaTeX Warning: File `{./img/atmosphere/need_more}.png' not found on input line 134. ! Package pdftex.def Error: File `./img/atmosphere/need_more.png' not found. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.134 ...xdimen]{{./img/atmosphere/need_more}.png} `NEED MORE?' button to re... (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] LaTeX Warning: File `{./img/atmosphere/project_icon}.png' not found on input li ne 238. ! Package pdftex.def Error: File `./img/atmosphere/project_icon.png' not found. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.238 ...men]{{./img/atmosphere/project_icon}.png} Overfull \hbox (3.50366pt too wide) in paragraph at lines 270--270 []\T1/phv/m/n/10 Ver- Overfull \hbox (3.75368pt too wide) in paragraph at lines 270--270 \T1/phv/m/n/10 sion| Overfull \hbox (7.32753pt too wide) in paragraph at lines 270--270 []\T1/phv/m/n/10 Link| Overfull \hbox (18.87273pt too wide) in paragraph at lines 270--270 []\T1/phv/m/n/10 Notes/other Overfull \hbox (3.42749pt too wide) in paragraph at lines 270--270 [][][]\T1/ptm/m/n/10 Im- Overfull \hbox (2.86757pt too wide) in paragraph at lines 270--270 \T1/ptm/m/n/10 age[][]| [5] LaTeX Warning: File `{./img/atmosphere/launch_window}.png' not found on input l ine 292. ! Package pdftex.def Error: File `./img/atmosphere/launch_window.png' not found . See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.292 ...en]{{./img/atmosphere/launch_window}.png} [6] [7] [8] Chapter 2. Overfull \hbox (9.49744pt too wide) in paragraph at lines 380--380 [] Underfull \hbox (badness 10000) in paragraph at lines 380--380 Underfull \hbox (badness 10000) in paragraph at lines 382--383 []\T1/ptm/m/n/10 Atmosphere Underfull \hbox (badness 10000) in paragraph at lines 385--386 []\T1/ptm/m/n/10 Check or Underfull \hbox (badness 10000) in paragraph at lines 385--386 \T1/ptm/m/n/10 re-quest Underfull \hbox (badness 10000) in paragraph at lines 385--386 \T1/ptm/m/n/10 Verse User Overfull \hbox (25.26727pt too wide) in paragraph at lines 395--395 [] Underfull \hbox (badness 10000) in paragraph at lines 395--395 Overfull \hbox (260.20543pt too wide) in paragraph at lines 397--402 [] Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 as-sumes Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 fa-mil-iar- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 ity with Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 iCom- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 mands. Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 wish to Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 com-plete Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 mands Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 tu-to-rial, Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 and you Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 to in-stall Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 iCom- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 a lo-cal Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 ma-chine Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 if you Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 want to Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 trans-fer Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 that ma- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 chine to Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 an At- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 mo-sphere ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.406 \item {} \begin{description} ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.407 ...ater{}{}`\_}}] \leavevmode\begin{itemize} Overfull \hbox (93.65704pt too wide) in paragraph at lines 407--408 [] Underfull \hbox (badness 10000) in paragraph at lines 407--408 Underfull \hbox (badness 10000) in paragraph at lines 409--410 [] Overfull \hbox (23.64784pt too wide) in paragraph at lines 409--410 \T1/ptm/b/n/10 `iCommands Underfull \hbox (badness 10000) in paragraph at lines 409--410 \T1/ptm/b/n/10 Down- Underfull \hbox (badness 10000) in paragraph at lines 409--410 \T1/ptm/b/n/10 load Underfull \hbox (badness 10000) in paragraph at lines 409--410 \T1/ptm/b/n/10 links Overfull \hbox (78.1466pt too wide) in paragraph at lines 425--425 [] Underfull \hbox (badness 10000) in paragraph at lines 425--425 Underfull \hbox (badness 10000) in paragraph at lines 427--430 []\T1/ptm/m/n/10 You Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 can Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 con-nect Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 via Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Web- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 shell Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 to an Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 At-mo- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 sphere Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 in- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 stance Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 a web Overfull \hbox (2.55814pt too wide) in paragraph at lines 427--430 \T1/ptm/m/n/10 browser. Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Al-ter- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 na- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 tively, Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 con-nect Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 via Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 SSH Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Linux Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 com- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 puter. Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 If you Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 are Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 us-ing Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Win- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 dows, Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 we Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 sug-gest Underfull \hbox (badness 6625) in paragraph at lines 427--430 \T1/ptm/m/n/10 a SSH Underfull \hbox (badness 10000) in paragraph at lines 432--433 [] Overfull \hbox (6.32813pt too wide) in paragraph at lines 432--433 \T1/ptm/m/n/10 Windows Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 com- Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 pat-i-ble Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 SSH Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 client Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 (Op- Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 tional) Overfull \hbox (67.29689pt too wide) in paragraph at lines 442--442 [] Underfull \hbox (badness 10000) in paragraph at lines 442--442 Overfull \hbox (268.26573pt too wide) in paragraph at lines 444--447 [] Overfull \hbox (19.55812pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 browser. Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 Al- Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 ter- Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 na- Overfull \hbox (8.02805pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 tively Overfull \hbox (0.64833pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 you Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 can Overfull \hbox (3.41823pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 con- Overfull \hbox (2.3081pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 nect Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 via Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 a Overfull \hbox (6.7582pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 VNC Overfull \hbox (8.16809pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 view- Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 ing Overfull \hbox (7.86789pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 client Overfull \hbox (3.97816pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 such Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 as Overfull \hbox (3.97803pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 Real Overfull \hbox (6.7582pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 VNC Overfull \hbox (14.5581pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 viewer. Underfull \hbox (badness 10000) in paragraph at lines 451--452 [] Overfull \hbox (10.05812pt too wide) in paragraph at lines 451--452 \T1/ptm/m/n/10 Download Underfull \hbox (badness 10000) in paragraph at lines 451--452 [][]\T1/ptm/m/n/10 Real Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 VNC Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 Viewer Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 your [9] Overfull \vbox (912.65993pt too high) has occurred while \output is active [10] No file CyVerseDocumentation.ind. Package sphinx Warning: ******** ERROR !! PLEASE UPDATE titlesec.sty !!******** ******** THIS VERSION SWALLOWS SECTION NUMBERS.********. [11] (./CyVerseDocumentation.aux) Package rerunfilecheck Warning: File `CyVerseDocumentation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (15 pages, 142072 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2017-06-10T03:17:38.389293Z, end-time: 2017-06-10T03:17:38.504382Z, duration: 0, exit-code: 0 makeindex -s python.ist CyVerseDocumentation.idx This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file CyVerseDocumentation.idx...done (0 entries accepted, 0 rejected). Nothing written in CyVerseDocumentation.ind. Transcript written in CyVerseDocumentation.ilg. [rtd-command-info] start-time: 2017-06-10T03:17:38.628558Z, end-time: 2017-06-10T03:17:39.196129Z, duration: 0, exit-code: 0 pdflatex -interaction=nonstopmode /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_build/latex/CyVerseDocumentation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/chec kouts/latest/_build/latex/CyVerseDocumentation.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 81 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2016/10/12 v1.5 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/fncychap/fncychap.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (./sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty) (/usr/share/texlive/texmf-dist/tex/latex/tabulary/tabulary.sty (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/threeparttable/threeparttable.sty) (./footnotehyper-sphinx.sty (/usr/share/texlive/texmf-dist/tex/latex/mdwtools/footnote.sty)) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/pdftex/pdfcolor.tex) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (./needspace.sty) ** (sphinx) defining (legacy) text style macros without \sphinx prefix ** if clashes with packages, set latex_keep_old_macro_names=False in conf.py (./sphinxhighlight.sty)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/multirow/multirow.sty) (/usr/share/texlive/texmf-dist/tex/latex/eqparbox/eqparbox.sty (/usr/share/texlive/texmf-dist/tex/latex/environ/environ.sty (/usr/share/texlive/texmf-dist/tex/latex/trimspaces/trimspaces.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file CyVerseDocumentation.idx (./CyVerseDocumentation.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./CyVerseDocumentation.out) (./CyVerseDocumentation.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./CyVerseDocumentation.toc) [1] [2] [1 <./cyverse_r gb.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3 <./atmosphere-ico n.png>] LaTeX Warning: File `{./img/atmosphere/need_more}.png' not found on input line 134. ! Package pdftex.def Error: File `./img/atmosphere/need_more.png' not found. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.134 ...xdimen]{{./img/atmosphere/need_more}.png} `NEED MORE?' button to re... (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4] LaTeX Warning: File `{./img/atmosphere/project_icon}.png' not found on input li ne 238. ! Package pdftex.def Error: File `./img/atmosphere/project_icon.png' not found. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.238 ...men]{{./img/atmosphere/project_icon}.png} Overfull \hbox (3.50366pt too wide) in paragraph at lines 270--270 []\T1/phv/m/n/10 Ver- Overfull \hbox (3.75368pt too wide) in paragraph at lines 270--270 \T1/phv/m/n/10 sion| Overfull \hbox (7.32753pt too wide) in paragraph at lines 270--270 []\T1/phv/m/n/10 Link| Overfull \hbox (18.87273pt too wide) in paragraph at lines 270--270 []\T1/phv/m/n/10 Notes/other Overfull \hbox (3.42749pt too wide) in paragraph at lines 270--270 [][][]\T1/ptm/m/n/10 Im- Overfull \hbox (2.86757pt too wide) in paragraph at lines 270--270 \T1/ptm/m/n/10 age[][]| [5] LaTeX Warning: File `{./img/atmosphere/launch_window}.png' not found on input l ine 292. ! Package pdftex.def Error: File `./img/atmosphere/launch_window.png' not found . See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.292 ...en]{{./img/atmosphere/launch_window}.png} [6] [7] [8] Chapter 2. Overfull \hbox (9.49744pt too wide) in paragraph at lines 380--380 [] Underfull \hbox (badness 10000) in paragraph at lines 380--380 Underfull \hbox (badness 10000) in paragraph at lines 382--383 []\T1/ptm/m/n/10 Atmosphere Underfull \hbox (badness 10000) in paragraph at lines 385--386 []\T1/ptm/m/n/10 Check or Underfull \hbox (badness 10000) in paragraph at lines 385--386 \T1/ptm/m/n/10 re-quest Underfull \hbox (badness 10000) in paragraph at lines 385--386 \T1/ptm/m/n/10 Verse User Overfull \hbox (25.26727pt too wide) in paragraph at lines 395--395 [] Underfull \hbox (badness 10000) in paragraph at lines 395--395 Overfull \hbox (260.20543pt too wide) in paragraph at lines 397--402 [] Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 as-sumes Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 fa-mil-iar- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 ity with Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 iCom- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 mands. Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 wish to Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 com-plete Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 mands Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 tu-to-rial, Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 and you Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 to in-stall Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 iCom- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 a lo-cal Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 ma-chine Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 if you Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 want to Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 trans-fer Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 that ma- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 chine to Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 an At- Underfull \hbox (badness 10000) in paragraph at lines 397--402 \T1/ptm/m/n/10 mo-sphere ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.406 \item {} \begin{description} ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.407 ...ater{}{}`\_}}] \leavevmode\begin{itemize} Overfull \hbox (93.65704pt too wide) in paragraph at lines 407--408 [] Underfull \hbox (badness 10000) in paragraph at lines 407--408 Underfull \hbox (badness 10000) in paragraph at lines 409--410 [] Overfull \hbox (23.64784pt too wide) in paragraph at lines 409--410 \T1/ptm/b/n/10 `iCommands Underfull \hbox (badness 10000) in paragraph at lines 409--410 \T1/ptm/b/n/10 Down- Underfull \hbox (badness 10000) in paragraph at lines 409--410 \T1/ptm/b/n/10 load Underfull \hbox (badness 10000) in paragraph at lines 409--410 \T1/ptm/b/n/10 links Overfull \hbox (78.1466pt too wide) in paragraph at lines 425--425 [] Underfull \hbox (badness 10000) in paragraph at lines 425--425 Underfull \hbox (badness 10000) in paragraph at lines 427--430 []\T1/ptm/m/n/10 You Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 can Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 con-nect Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 via Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Web- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 shell Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 to an Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 At-mo- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 sphere Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 in- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 stance Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 a web Overfull \hbox (2.55814pt too wide) in paragraph at lines 427--430 \T1/ptm/m/n/10 browser. Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Al-ter- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 na- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 tively, Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 con-nect Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 via Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 SSH Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Linux Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 com- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 puter. Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 If you Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 are Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 us-ing Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 Win- Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 dows, Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 we Underfull \hbox (badness 10000) in paragraph at lines 427--430 \T1/ptm/m/n/10 sug-gest Underfull \hbox (badness 6625) in paragraph at lines 427--430 \T1/ptm/m/n/10 a SSH Underfull \hbox (badness 10000) in paragraph at lines 432--433 [] Overfull \hbox (6.32813pt too wide) in paragraph at lines 432--433 \T1/ptm/m/n/10 Windows Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 com- Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 pat-i-ble Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 SSH Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 client Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 (Op- Underfull \hbox (badness 10000) in paragraph at lines 432--433 \T1/ptm/m/n/10 tional) Overfull \hbox (67.29689pt too wide) in paragraph at lines 442--442 [] Underfull \hbox (badness 10000) in paragraph at lines 442--442 Overfull \hbox (268.26573pt too wide) in paragraph at lines 444--447 [] Overfull \hbox (19.55812pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 browser. Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 Al- Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 ter- Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 na- Overfull \hbox (8.02805pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 tively Overfull \hbox (0.64833pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 you Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 can Overfull \hbox (3.41823pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 con- Overfull \hbox (2.3081pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 nect Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 via Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 a Overfull \hbox (6.7582pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 VNC Overfull \hbox (8.16809pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 view- Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 ing Overfull \hbox (7.86789pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 client Overfull \hbox (3.97816pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 such Underfull \hbox (badness 10000) in paragraph at lines 444--447 \T1/ptm/m/n/10 as Overfull \hbox (3.97803pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 Real Overfull \hbox (6.7582pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 VNC Overfull \hbox (14.5581pt too wide) in paragraph at lines 444--447 \T1/ptm/m/n/10 viewer. Underfull \hbox (badness 10000) in paragraph at lines 451--452 [] Overfull \hbox (10.05812pt too wide) in paragraph at lines 451--452 \T1/ptm/m/n/10 Download Underfull \hbox (badness 10000) in paragraph at lines 451--452 [][]\T1/ptm/m/n/10 Real Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 VNC Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 Viewer Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 451--452 \T1/ptm/m/n/10 your [9] Overfull \vbox (912.65993pt too high) has occurred while \output is active [10] (./CyVerseDocumentation.ind) Package sphinx Warning: ******** ERROR !! PLEASE UPDATE titlesec.sty !!******** ******** THIS VERSION SWALLOWS SECTION NUMBERS.********. [11] (./CyVerseDocumentation.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on CyVerseDocumentation.pdf (15 pages, 143844 bytes). Transcript written on CyVerseDocumentation.log. [rtd-command-info] start-time: 2017-06-10T03:17:39.309754Z, end-time: 2017-06-10T03:17:39.365790Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_build/latex/CyVerseDocumentation.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/artifacts/latest/sphinx_pdf/cyverse-atmosphere-guide.pdf [rtd-command-info] start-time: 2017-06-10T03:17:39.583462Z, end-time: 2017-06-10T03:17:40.591438Z, duration: 1, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.5.3 making output directory... loading translations [en]... done loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [epub]: targets for 3 source files that are out of date updating environment: 3 added, 0 changed, 0 removed reading sources... [ 33%] index reading sources... [ 66%] step1 reading sources... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step3' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step4' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:21: WARNING: toctree contains reference to nonexisting document u'step5' /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:68: ERROR: Unknown target name: "icommands quick start <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:69: ERROR: Unknown target name: "icommands download links <>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step1.rst:94: WARNING: image file not readable: ./img/atmosphere/need_more.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:159: WARNING: image file not readable: ./img/atmosphere/project_icon.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/step2.rst:162: WARNING: image file not readable: ./img/atmosphere/launch_window.png looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: self referenced toctree found. Ignored. done writing output... [ 33%] index writing output... [ 66%] step1 writing output... [100%] step2 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index generating indices... genindex writing additional pages... copying images... [ 33%] ./img/atmosphere/atmosphere-icon.png copying images... [ 66%] ./img/homeicon.png copying images... [100%] ./img/cyverse_rgb.png copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_static' does not exist WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing nav.xhtml file... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing toc.ncx file... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/index.rst:: WARNING: circular toctree references detected, ignoring: index <- index writing YOURPROJECTNAMEHEREastopic_tutorial.epub file... build succeeded, 18 warnings. [rtd-command-info] start-time: 2017-06-10T03:17:40.746713Z, end-time: 2017-06-10T03:17:40.800858Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/checkouts/latest/_build/epub/YOURPROJECTNAMEHEREastopic_tutorial.epub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-atmosphere-guide/artifacts/latest/sphinx_epub/cyverse-atmosphere-guide.epub